But the German chancellor told parliament she would not tolerate criticism "at home or abroad" until the full details of the incident were known, and said the German army's presence in Afghanistan was "in the urgent interest of our country".

Merkel's comments came as Nato acknowledged for the first time that Afghan civilians were among those killed when German commanders called in US jets to attack two stolen oil tankers near Kunduz on Friday. The death toll has not been established, but Afghan Rights Monitor, a national watchdog group, said that between 60 and 70 villagers had been killed.

A statement today from the Nato-led International Security Assistance Force said that commanders originally believed the tankers were surrounded only by Taliban insurgents, but a subsequent review showed "civilians also were killed and injured in the strike".

The air strike – the deadliest military operation German troops have been involved in since the second world war – has caused a rift between German and US authorities over the conduct of the war, and prompted a fierce reaction from the Afghan government. The new US commander in Afghanistan, General Stanley McChrystal, who had sought to distance himself from the incident, today appointed a Canadian general to investigate the incident.

Addressing a special sitting of parliament, Merkel acknowledged that civilians may have been harmed, but said that contradictory reports of the incident meant that the victims had still not been identified.

"We will not accept premature judgments," she said. "I say this very clearly after what I have experienced in the last few days: I will not tolerate that from whoever it may be, at home as well as abroad."

Less than three weeks before a general election, the attack has also become a major political issue in Berlin.

Merkel resisted calls from the Left party for an immediate withdrawal of German troops, but she said Nato allies should define a "clear goal" by the end of the year regarding a "handover strategy".

The government, which has referred to its Afghanistan policy as a "stabilisation effort" and has avoided using the word "war", has come under pressure from all parties to talk with more honesty to the electorate about the conflict.

Jürgen Trittin, of the Green party, delivered a blistering attack on the government, calling the raid a "breaking point that clearly shows that Germany has shifted its strategy on Afghanistan and in my view, in the wrong direction".

Addressing the embattled defence minister, Franz Josef Jung, who has faced calls for his resignation in the light of the incident, which he referred to yesterdayas "militarily necessary", Trittin said: "You obviously work on the principle hush it up, deny it, and when there's no alternative, I'll eventually apologise."

Germany's foreign minister, Frank-Walter Steinmeier, of the Social Democrats, told the Bundestag it would be "irresponsible" for German troops simply to pull out of Afghanistan. But he added: "The Bundeswehr is not an occupying force. We're not there for eternity."

Sign up for the Guardian Today

Our editors' picks for the day's top news and commentary delivered to your inbox each morning.